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Initial commit of the files to transition the build process to using the CMake tool
1 parent ca5adc2 commit 6ca4c57

11 files changed

Lines changed: 521 additions & 102 deletions

‎.gitignore‎

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*.rnapoly
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*.rnasubopt
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build/
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build/*
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include/pmfe_build_config.h
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wrapper-runner-script/PMFECommandRunner.sh
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wrapper-runner-script/PMFEDeveloperCommandRunner.sh
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‎Makefile‎

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This file was deleted.

‎Makefile.generic_unix‎

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# source files
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SRC := $(wildcard src/*.cc)
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OBJ := $(SRC:.cc=.o)
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BINSRC := $(wildcard src/bin-*.cc)
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BINOBJ := $(BINSRC:.cc=.o)
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TESTSRC := $(wildcard src/test-*.cc)
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TESTOBJ := $(TESTSRC:.cc=.o)
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LIBOBJ := $(OBJ)
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LIBOBJ := $(filter-out $(BINOBJ),$(LIBOBJ))
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LIBOBJ := $(filter-out $(TESTOBJ),$(LIBOBJ))
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DEP := $(SRC:.cc=.P)
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HDR := $(wildcard src/*.h)
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# include directories
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INCLUDES += -IiB4e
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INCLUDES += -I/usr/local/include # For Homebrew
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# C++ compiler flags
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CXXFLAGS += -Wall -fvisibility=hidden -fvisibility-inlines-hidden -frounding-math -DABI=0
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CXXFLAGS += -fPIC
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CXXFLAGS += -fopenmp
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CXXFLAGS += -Wall
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CXXFLAGS += -g
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CXXFLAGS += -O3
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CXXFLAGS += -Iinclude $(INCLUDES) -I$(shell readlink -f ../cgal/*/include | tr "\n" " " | sed -e 's/ / -I/g') \
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-DBOOST_FILESYSTEM_NO_DEPRECATED \
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-I$(shell readlink -f ../BoostLocalInstall/include) \
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-DCGAL_HEADER_ONLY -UBOOST_DISABLE_THREADS -DBOOST_LOG_DYN_LINK -BOOST_ALL_DYN_LINK \
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$(shell pkg-config gmp --cflags) $(shell pkg-config gmpxx --cflags)
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CXXFLAGS_BASE := $(CXXFLAGS)
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CXX_STDV11= -std=c++11 -D_GLIBCXX_USE_CXX11_ABI=1
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CXX_STDV0X= -std=c++11 -D_GLIBCXX_USE_CXX11_ABI=0
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# library paths
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LIBS += -L/usr/local/lib # For Homebrew
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LIBS += -L/opt/rh/devtoolset-9/root/usr/lib/gcc/x86_64-redhat-linux/9 -lstdc++
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LIBS += $(shell pkg-config gmp --libs) $(shell pkg-config gmpxx --libs)
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LIBS += -L$(shell readlink -f ../BoostLocalInstall/lib)
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LIBS += -lm
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LIBS += -lboost_filesystem
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LIBS += -lboost_program_options
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LIBS += -lboost_system
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LIBS += -lboost_log
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LIBS += -frounding-math -lboost_log_setup -lboost_thread -lboost_atomic -lboost_regex -lboost_chrono
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LIBS += -Wl,-Bdynamic -lpthread
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#LIBS += -Wl,--no-undefined -Wl,--no-allow-shlib-undefined
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BIN = pmfe-findmfe pmfe-scorer pmfe-parametrizer pmfe-subopt pmfe-tests
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all: $(OBJ) bin_prereqs $(BIN)
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-include $(DEP)
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debug: CXXFLAGS += -Og
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debug: all
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bin_prereqs:
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@mkdir -p bin
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## Note we are having to (re)set the C++ standard to get compatibility in the
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## broken, non-cohesive feature sets on the local compiler. This is not an
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## exact science, but rather success by trial and error (Sigh.)
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pmfe-findmfe: CXXFLAGS:= $(CXX_STDV0X) $(CXXFLAGS_BASE)
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pmfe-findmfe: $(LIBOBJ) src/bin-findmfe.o
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$(CXX) $(CXXFLAGS) $^ $(LIBS) -o bin/$@
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pmfe-scorer: CXXFLAGS:= $(CXX_STDV0X) $(CXXFLAGS_BASE)
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pmfe-scorer: $(LIBOBJ) src/bin-scorer.o
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$(CXX) $(CXXFLAGS) $^ $(LIBS) -o bin/$@
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pmfe-parametrizer: CXXFLAGS:= $(CXX_STDV0X) $(CXXFLAGS_BASE)
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pmfe-parametrizer: $(LIBOBJ) src/bin-parametrizer.o
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$(CXX) $(CXXFLAGS) $^ $(LIBS) -o bin/$@
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pmfe-subopt: CXXFLAGS:= $(CXX_STDV0X) $(CXXFLAGS_BASE)
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pmfe-subopt: $(LIBOBJ) src/bin-subopt.o
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$(CXX) $(CXXFLAGS) $^ $(LIBS) -o bin/$@
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pmfe-tests: CXXFLAGS:= $(CXX_STDV0X) $(CXXFLAGS_BASE)
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pmfe-tests: $(LIBOBJ) $(TESTOBJ) src/bin-tests.o
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$(CXX) $(CXXFLAGS) $^ $(LIBS) -o bin/$@
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%.o: %.cc
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$(CXX) -MD $(CXX_STDV0X) $(CXXFLAGS) $(INCLUDES) -o $@ -c $<
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@cp $*.d $*.P; \
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sed -e 's/#.*//' -e 's/^[^:]*: *//' -e 's/ *\\$$//' \
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-e '/^$$/ d' -e 's/$$/ :/' < $*.d >> $*.P; \
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rm -f $*.d
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clean:
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-rm -vf $(EXEC) $(OBJ) $(DEP) $(BIN)
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install:
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uninstall:
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.PHONY: clean

‎cmake/AutogenBuildConfigHeader.cmake‎

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#### AutogenBuildConfigHeader.cmake : Create the PMFE build config header.
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#### Author: Maxie D. Schmidt (github.com/maxieds)
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#### Created: 2020.11.02
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## Set the absolute location of the path to the PMFE sources:
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if(APPLE)
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execute_process (
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COMMAND bash -c "greadlink -f ."
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OUTPUT_VARIABLE BuildAbsPath
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)
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elseif(UNIX AND NOT APPLE)
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execute_process (
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COMMAND bash -c "readlink -f ."
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OUTPUT_VARIABLE BuildAbsPath
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)
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endif()
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## Set the build time datestamp for reference:
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execute_process (
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COMMAND bash -c "date +'%F @ %T%p (%Y.%m.%d-%H%M%S)'"
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OUTPUT_VARIABLE BuildTimeStamp
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)
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## Create a record of which GitHub commit or tag the PMFE sources reference:
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execute_process (
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COMMAND bash -c "git --no-pager log -1 --format='%H [-- %h --]'"
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OUTPUT_VARIABLE BuildGitCommitHash
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)
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execute_process (
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COMMAND bash -c "git --no-pager log -1 --format='%ai'"
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OUTPUT_VARIABLE BuildGitCommitDate
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)
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## Define all of the file placeholders we will substitute the live configuration data into:
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## Syntax: "[SUBST_PLACEHOLDER_NAME]->ActualValue" denotes that we will replace the string
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## '${SUBST_PLACEHOLDER_NAME}' with 'ActualValue' below.
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list(APPEND PMFEConfigHeaderSubstsList "[CMAKE_VERSION]->${CMAKE_VERSION}")
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list(APPEND PMFEConfigHeaderSubstsList "[CMAKE_SYSTEM_VERSION]->${CMAKE_SYSTEM_VERSION}")
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list(APPEND PMFEConfigHeaderSubstsList "[CMAKE_SYSTEM_PROCESSOR]->${CMAKE_SYSTEM_PROCESSOR}")
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list(APPEND PMFEConfigHeaderSubstsList "[CMAKE_HOST_SYSTEM_NAME]->${CMAKE_HOST_SYSTEM_NAME}")
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list(APPEND PMFEConfigHeaderSubstsList "[CMAKE_C_FLAGS]->${CMAKE_C_FLAGS}")
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list(APPEND PMFEConfigHeaderSubstsList "[CMAKE_CXX_FLAGS]->${CMAKE_CXX_FLAGS}")
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list(APPEND PMFEConfigHeaderSubstsList "[CMAKE_BUILD_TYPE]->${CMAKE_BUILD_TYPE}")
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list(APPEND PMFEConfigHeaderSubstsList "[CMAKE_EXE_LINKER_FLAGS]->${CMAKE_EXE_LINKER_FLAGS}")
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list(APPEND PMFEConfigHeaderSubstsList "[CMAKE_SHARED_LINKER_FLAGS]->${CMAKE_SHARED_LINKER_FLAGS}")
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list(APPEND PMFEConfigHeaderSubstsList "[PMFE_PACKAGE_NAME]->${PMFE_PACKAGE_NAME}")
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list(APPEND PMFEConfigHeaderSubstsList "[PMFE_PACKAGE_VERSION]->${PMFE_PACKAGE_VERSION}")
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list(APPEND PMFEConfigHeaderSubstsList "[PMFE_PACKAGE_STRING]->${PMFE_PACKAGE_STRING}")
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list(APPEND PMFEConfigHeaderSubstsList "[PMFE_BUILD_GIT_COMMIT_HASH]->${BuildGitCommitHash}")
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list(APPEND PMFEConfigHeaderSubstsList "[PMFE_BUILD_GIT_COMMIT_DATE]->${BuildGitCommitDate}")
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list(APPEND PMFEConfigHeaderSubstsList "[PMFE_BUILD_DATESTAMP]->${BuildTimeStamp}")
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list(APPEND PMFEConfigHeaderSubstsList "[PMFE_BUILD_ABS_WORKING_DIR]->${BuildAbsPath}")
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## Copy the stub header file to the build-time location:
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set(PMFEBuildConfigHeaderStubPath "${buildAbsPath}/include/pmfe_build_config.h.in")
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set(PMFEBuildConfigNewHeaderPath "${buildAbsPath}/include/pmfe_build_config.h")
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file(
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COPY ${PMFEBuildConfigHeaderStubPath}
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DESTINATION ${PMFEBuildConfigNewHeaderPath}
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)
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## Substitute the placeholders in that file with the live build config information:
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function(Func_substPMFEConfigHeaderParam "${SUBST_VAR_NAME}" "${SUBST_VAR_VALUE}")
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message(DEBUG "Substituting ${SUBST_VAR_NAME} -> ${SUBST_VAR_VALUE} in ${PMFEBuildConfigNewHeaderPath} ...")
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execute_process (
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COMMAND bash -c "sed -i 's/\$\{${SUBST_VAR_NAME}\}/${SUBST_VAR_VALUE}/' ${PMFEBuildConfigNewHeaderPath}"
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)
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endfunction(Func_substPMFEConfigHeaderParam)
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function(Func_substPMFEConfigHeaderParamFromSpec "${FULL_CONFIG_SUBST_SPEC}")
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string(REGEX "(\[[^\ ]+\])->" funcInput_localParamName "${FULL_CONFIG_SUBST_SPEC}")
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string(REGEX "->[^\ ]+$" funcInput_localParamValue "${FULL_CONFIG_SUBST_SPEC}")
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Func_substPMFEConfigHeaderParam("${funcInput_localParamName}" "${funcInput_localParamValue}")
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endfunction(Func_substPMFEConfigHeaderParamFromSpec)
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foreach(PMFE_CONFIG_HEADER_SUBST_SPEC ${PMFEConfigHeaderSubstsList})
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Func_substPMFEConfigHeaderParamFromSpec("${PMFE_CONFIG_HEADER_SUBST_SPEC}")
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endforeach()

‎cmake/PostBuildAutogenWrapperScript.cmake‎

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#### PostBuildAutogenWrapperScript.cmake : Create the post-build wrapper / runner script source
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#### to run the PMFE utilities with the correct
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#### absolute paths local to this build.
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#### Author: Maxie D. Schmidt (github.com/maxieds)
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#### Created: 2020.11.02
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## Set the absolute location of the path to the PMFE sources:
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if(APPLE)
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execute_process (
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COMMAND bash -c "greadlink -f ."
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OUTPUT_VARIABLE BuildAbsPath
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)
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elseif(UNIX AND NOT APPLE)
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execute_process (
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COMMAND bash -c "readlink -f ."
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OUTPUT_VARIABLE BuildAbsPath
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)
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endif()
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## Set the build time datestamp for reference:
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execute_process (
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COMMAND bash -c "date +'%F @ %T%p (%Y.%m.%d-%H%M%S)'"
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OUTPUT_VARIABLE BuildTimeStamp
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)
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## Create a record of which GitHub commit or tag the PMFE sources reference:
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execute_process (
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COMMAND bash -c "git --no-pager log -1 --format='%H [-- %h --]'"
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OUTPUT_VARIABLE BuildGitCommitHash
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)
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execute_process (
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COMMAND bash -c "git --no-pager log -1 --format='%ai'"
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OUTPUT_VARIABLE BuildGitCommitDate
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)
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## Define all of the file placeholders we will substitute the live configuration data into:
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## Syntax: "[SUBST_PLACEHOLDER_NAME]->ActualValue" denotes that we will replace the string
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## '${SUBST_PLACEHOLDER_NAME}' with 'ActualValue' below.
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list(APPEND PMFEWrapperRunnerScriptSubstsList "[PMFE_BUILD_TIMESTAMP]->${BuildTimeStamp}")
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list(APPEND PMFEWrapperRunnerScriptSubstsList "[PMFE_BUILD_GIT_COMMIT_HASH]->${BuildGitCommitHash}")
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list(APPEND PMFEWrapperRunnerScriptSubstsList "[PMFE_BUILD_GIT_COMMIT_DATE]->${BuildGitCommitDate}")
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list(APPEND PMFEWrapperRunnerScriptSubstsList "[PMFE_BUILD_ABS_BINARY_DIR_PATH]->${BuildAbsPath}")
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## Copy the stub header file to the build-time location:
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set(PMFEWrapperRunnerScriptStubPath "${buildAbsPath}/wrapper-runner-script/PMFECommandRunner.sh.in")
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set(PMFEWrapperRunnerScriptNewPath "${buildAbsPath}/wrapper-runner-script/PMFECommandRunner.sh")
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file(
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COPY ${PMFEWrapperRunnerScriptStubPath}
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DESTINATION ${PMFEWrapperRunnerScriptNewPath}
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)
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set(PMFEWrapperDevRunnerScriptStubPath "${buildAbsPath}/wrapper-runner-script/PMFEDeveloperCommandRunner.sh.in")
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set(PMFEWrapperDevRunnerScriptNewPath "${buildAbsPath}/wrapper-runner-script/PMFEDeveloperCommandRunner.sh")
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file(
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COPY ${PMFEWrapperDevRunnerScriptStubPath}
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DESTINATION ${PMFEWrapperDevRunnerScriptNewPath}
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)
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## Substitute the placeholders in that file with the live build config information:
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function(Func_substPMFEWrapperRunnerScriptParam "${SUBST_VAR_NAME}" "${SUBST_VAR_VALUE}" "${OUTFILE_PATH}")
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message(DEBUG "Substituting ${SUBST_VAR_NAME} -> ${SUBST_VAR_VALUE} in ${OUTFILE_PATH} ...")
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execute_process (
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COMMAND bash -c "sed -i 's/\$\{${SUBST_VAR_NAME}\}/${SUBST_VAR_VALUE}/' ${OUTFILE_PATHh}"
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)
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endfunction(Func_substPMFEConfigHeaderParam)
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function(Func_substPMFEWrapperRunnerScriptParamFromSpec "${FULL_CONFIG_SUBST_SPEC}" "${OUTFILE_PATH}")
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string(REGEX "(\[[^\ ]+\])->" FuncInput_localParamName "${FULL_CONFIG_SUBST_SPEC}")
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string(REGEX "->[^\ ]+$" FuncInput_localParamValue "${FULL_CONFIG_SUBST_SPEC}")
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Func_substPMFEWrapperRunnerScriptParam(
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"${FuncInput_localParamName}"
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"${FuncInput_localParamValue}"
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"${OUTFILE_PATH}"
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)
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endfunction(Func_substPMFEConfigHeaderParamFromSpec)
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foreach(PMFE_RUNNER_SCRIPT_SUBST_SPEC ${PMFEWrapperRunnerScriptSubstsList} "${OUTFILE_PATH}")
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Func_substPMFEWrapperRunnerScriptParamFromSpec(
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"${PMFE_RUNNER_SCRIPT_SUBST_SPEC}"
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"${PMFEWrapperRunnerScriptNewPath}"
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)
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Func_substPMFEWrapperRunnerScriptParamFromSpec(
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"${PMFE_RUNNER_SCRIPT_SUBST_SPEC}"
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"${PMFEWrapperDevRunnerScriptNewPath}"
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)
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endforeach()
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message(STATUS "Installed the autogenerated wrapper (binary runner) scripts into: ")
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message(STATUS " >> \"${PMFEWrapperRunnerScriptNewPath}\" [user runner script]")
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message(STATUS " >> \"${PMFEWrapperRunnerDevScriptNewPath}\" [developer script]\n")

‎include/nndb_constants.h‎

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#ifndef _NNDB_CONSTANTS_H
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#define _NNDB_CONSTANTS_H
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#include "pmfe_build_config.h"
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#include "pmfe_types.h"
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#include "rational.h"
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class Turner99: public NNDBConstants {
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public:
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Turner99(const ParameterVector& params = ParameterVector(), const fs::path& param_dir = "Turner99");
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Turner99(const ParameterVector& params = ParameterVector(), const fs::path& param_dir = PMFEBuild::TURNER99_DATA_DIR);
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protected:
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void initMiscValues(const fs::path& param_dir);

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